DreINT0013239 @ danRer10
Intron Retention
Gene
ENSDARG00000104868 | KCNT1 (2 of 2)
Description
potassium channel, sodium activated subfamily T, member 1 [Source:HGNC Symbol;Acc:HGNC:18865]
Coordinates
chr5:64837752-64839201:+
Coord C1 exon
chr5:64837752-64837932
Coord A exon
chr5:64837933-64839036
Coord C2 exon
chr5:64839037-64839201
Length
1104 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAG
5' ss Score
6.66
3' ss Seq
TTCTGTCTTTTTCACACCAGTTC
3' ss Score
7.46
Exon sequences
Seq C1 exon
GGCTTGTGGGATTCAGCACCTGGAGCGAGCAGGGAAGAATCTGACACTCTTTGACGCTTTATATTTCTGCATCGTCACCTTCTCCACTGTTGGATATGGAGATGTGACGCCCAGAATCTGGCCCTCTCAGCTGCTGGTGGTCATCATGATCTGTGTGGCGCTGGTGGTGCTGCCATTACAG
Seq A exon
GTGAAGGATTATCATTGCTTTGACACAAAATGCATTCAATAGATACAGTTGAAGTCAGAATTATTAGCCCGCTGTATATTTTTCCTTCAATAACATTTTTTTCAACACATTTCTAAACAAAATAGAACTAATTTCTAATAACTGATTGATTTTATCTTTGCCATGAGGACAGTATATTATATTTGACTAGATATTTTTCAAGATATTAGTATTCAGCTTAAAGTGCAAATTAAAAGCGTAACTAGGTTAATTAGGGTAATTAGGCACATCATCGTATTACAATGGTTAGTTCTGTAGACAATCGAAAAAATATATAGCTTAAGGGGGCTAATAATGACCTTAAAATGTTTTCTTTAAAAATTAAAAACTGCTTTTATTCTAGCCGAAATAAAACAAAAAGTAAAGACTTTCTCCAGAAGAAAAAAATATTATAGGAAGTACTGCAAAAATGTAATTGCTCTGTTAAACATCCTTTGGGAAATATTTGAAAATTTACAAAAAAAATAACAGGAGGGCGAATAATTCTGACTTCAACTGTATGTTTCCATTCAAAGATGTTAATTAGACTTATGCGCAAAACTGAATAATTACATTAAACATTTGTGAATAAATGCATTGTTTCCATCCAGAACAATTGAAAGATTTTTGAAAGCGACCCAAGTCACGGCTGAATGCTGGTCCTCTCACTCATGTCATTTCTCTCTGTCTGCCTGTCTGTTGCCAAACACAGAGCGGGGGAGCTCTTGGCTCCGCCCACTTGTTACATTGAGCGAGAAGCAGAAACTAATTTTCATGTGAAGCAACATGCACCTAAAACAGCGAGCTGTGTACACACCCCCAACATGACACTTTTGAACACATTATAATAAAAACATCTGAACTGTGTGTTGAACTGAACCTAAACTGGCACACTCAGAACAACCATAATACTAATATTAAATCATAAAAAAAGGGGTAAACTGCCCTTTAAAAGTATGTTGAAGTACGTAGTTTTTGTACTTTTACAAATATGTAGGCTGAAACATGTATCTCCAATGAGCCTGTGTTGCATAAACAAGTGGAATTGCTAATAATTCACAGTACTTTCTGTCTTTTTCACACCAG
Seq C2 exon
TTCGAGGAGTTGGCGTATCTATGGATGGAGAGGCAGAAGTCAGGTGGAAACTACAGCAGACACCGCGCTCAGACAGAGAAACACGTGGTGCTCTGCGTCACCTCACTCAAAATAGACCTGCTCATGGATTTCCTCAATGAGTTCTATGCCCACCCGAGACTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000104868:ENSDART00000161567:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0788511=Ion_trans_2=FE(85.7=100)
A:
NA
C2:
PF0788511=Ion_trans_2=PD(11.5=16.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTGTGGGATTCAGCACCTGG
R:
TGTAGTCTCGGGTGGGCATAG
Band lengths:
343-1447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]